mirror of https://github.com/msberends/AMR.git
38 lines
2.0 KiB
R
38 lines
2.0 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("pca.R")
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test_that("PCA works", {
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library(dplyr)
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resistance_data <- example_isolates %>%
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filter(mo %in% as.mo(c("E. coli", "K. pneumoniae", "S. aureus"))) %>%
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select(mo, AMC, CXM, CTX, TOB, TMP) %>%
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group_by(order = mo_order(mo), # group on anything, like order
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genus = mo_genus(mo)) %>% # and genus as we do here
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summarise_if(is.rsi, resistance, minimum = 0)
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expect_s3_class(pca(resistance_data), "prcomp")
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expect_s3_class(prcomp(resistance_data), "prcomp")
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ggplot_pca(pca(resistance_data), ellipse = TRUE)
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})
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